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JLSteenwyk / ClipKIT

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
https://jlsteenwyk.com/ClipKIT/
MIT License
61 stars 4 forks source link

extract parsimony sites #25

Closed atongsa closed 1 year ago

atongsa commented 1 year ago

Dear author,

i use the command below to extract parsimony sites,

clipkit -l -m kpi-gappy i.fa -o o.fa

but get much more sites than the really parsimony sites,

i wonder does clipkit calculate gap(N/-) as variable sites when counting parsimony sites;

JLSteenwyk commented 1 year ago

Hi @atongsa,

Thank you so much for using ClipKIT. Can you please email me an exemplary input file? I would be more than happy to test it out. My email is jlsteenwyk@berkeley.com. Please include the version of ClipKIT you are using in your email.

Thanks again for using ClipKIT.

best,

Jacob